


Difficult Decisions

by AweburnPhoenix



Category: The X-Files
Genre: Aliens, Alternate Universe - Canon Divergence, Episode: s06e01 The Beginning, F/M, Gen, Kidnapping, Season/Series 06, Thriller
Language: English
Status: Completed
Published: 2019-11-01
Updated: 2019-11-01
Packaged: 2021-01-17 12:47:30
Rating: General Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 3,171
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/21267854
Author URL: https://archiveofourown.org/users/AweburnPhoenix/pseuds/AweburnPhoenix
Summary: Walter Skinner's family is threatened by the decisions he has to take.} » Audio version available on the Audio Fanfic Podcasthere
Relationships: Arlene/Walter Skinner
Comments: 7
Kudos: 15
Collections: X-Files Spooky Halloween Fanfic Exchange (2019)





	Difficult Decisions

**Author's Note:**

  * For [Billie1](https://archiveofourown.org/users/Billie1/gifts).

> Written for the X-Files "Spooky Fanfic Exchange (2019)". The prompt word was "aliens" and additional requests were S6, Skinner/Arlene, AU, Thriller, Romance & baby/family.
> 
> Dear Billie, I hope the wait is worth it.  
I tried to fit all of your tags in there in some way or another :)  
This was my first Skinner centered story, and I had so much fun writing it, thanks so much for the prompt!! I wish I could have had more time to explore it deeper.
> 
> Huge infinite thanks to Val and Jeri for her beta help; you girls rock <3
> 
> } » Audio version available on the Audio Fanfic Podcast [here](https://soundcloud.com/audiofanficpod/xf-difficult-decisions-by-aweburnphoenix)

> _“Mulder?” _Walter’s voice faltered on the answering machine. _“They took the kid. Mulder, They took my child!”_
> 
> He should have known better than trying to get the _white-picket-fence life_ while fighting the government.

* * *

** _ March 15, 1996_ **

** _ The Headless Woman’s Pub, Washington DC_ **

It was too much to handle. Walter Skinner decided to call it a day and drown his sorrows at his usual bar. He didn’t care if it was crowded with fellow FBI Agents; being Assistant Director gave one the prerogative to not be stared at the end of the day.

He was on his second glass of Scotch when he smelt a female essence by his right side. _Not again_, he pleaded and turned slightly to his left, leaning heavily on his right arm.

“Mr. Skinner?” a melodious voice sounded doubtful at his back. “I’m so sorry for your loss.”

So, the word was out. His private life was not private anymore.

Walter turned around to find a redhead sitting by his side. Arlene… something, he couldn’t remember her surname. She was AD Maslin’s assistant. Walter didn’t walk through the third floor that much, but whenever he did, the woman caught his eye. Every time, he had been ashamed of himself for he had still been a married man, even though it was his fault for refusing to sign the damn papers. Exactly why he had stalled for so long, he still had no clue. He had wanted to fix things with Sharon but, at the same time, he knew it wasn’t going anywhere. Where had the love gone? Maybe it had never been there.

“You ok, Sir?” Arlene asked, placing a hand on his shoulder, and he was brought back to the present. “You look so pale, should I call an ambulance or something?

“No, I’m fine, thank you. Just a bad week,” he added, gulping down the rest of his drink.

Arlene squeezed his bicep as a sign of understanding, and he wondered if there was something more to it.

If he were to admit the truth, he wouldn’t mind taking her home with him. But was it too soon? Should he get involved with someone from work? She wasn’t an agent or working in his department, so there wouldn’t be any problem with that. Maybe he was just imagining things. How many drinks had he had? Pushing the thought away, he stood up, ready to leave, but lost his balance, almost tripping over. Arlene managed to catch him and helped him stabilize.

“Do you need a ride home?” She offered, her intentions unmistakable this time.

“Yes, thank you, that would be nice.”

* * *

** _ August 22, 1997 _ **

** _ FBI HQ_ **

Walter would miss Kimberly dearly, she had probably been the best assistant he had ever had. Always quick and organized, no wonder she had been in the director’s office. Silver lining, he got to choose his new assistant, and Arlene’s name was on the top of the list. HR had had no problem with it since it didn’t imply any favoritism. Her pay would be the same, as well as her status. He would just get to see more of her, which always was good news.

“Lost in thought again?” he turned around to see her walking into his office lobby and walked over briskly to grab the cardboard box she was holding.

“You shouldn’t be carrying any weight in your state,” he admonished her lightly, refraining from kissing her, trying to keep his distance and stay professional.

“I’m only six months pregnant, it’s no biggie,” Arlene smiled, walking behind him while starting to unpack her things onto her new workspace.

He stood looking at her for longer than he should, but he couldn’t help it. It seemed that life was getting easier and happier lately.

Quick and strong heeled footsteps in the corridor reminded him that it was not exactly like that. Walter saw the red-haired woman walking fast, as she always did, as was reminded that he was dirty to the hilt. He should have let Agent Mulder carry the guilt, but he just couldn’t. The pair had helped him and, somehow, he found it his duty to take care of them this time.

“Agent Scully,” he called her from his door. 

As she turned around, he noticed her lately wilted face looking livelier. 

It made him smile. 

“How are you feeling these days?” Walter made it his duty to ask her every once in a while, as she was the quiet type and hardly ever reported on her health. How could Agent Mulder keep her running around the country in her state?

“I’m fine, Sir. The current round of treatment seems to be working better. Thanks for asking.”

“I’m glad to hear that. Keep me posted,” he dismissed her quickly and in a rush, she turned and was off.

“She’s pretty,” Arlene mentioned as soon as he was back into his lobby.

“Yes, she is,” there was no need in denying it. Lots of agents and students had been trapped by her looks, and nonetheless, she remained being _Mrs. Spooky_. “But she is taken. And so am I,” he quickly added, kissing her ring finger. They hadn’t tied the knot, but it was a mere formality.

“So the rumors about her and Agent Mulder…”

“No, no, still rumors. But I doubt they’ll ever be able to be with anybody but each other with all the shit they’ve seen.”

He remembered himself after the war. How all the death and horrors had changed him. The last few months, being immersed in the X-Files more than he usually did, had made him realize the line of work Agents Mulder and Scully devoted their time to was not for the faint of heart.

“I got work to do,” he finally said, walking into his office. “Let me know if you need anything, dear.”

* * *

** _November 20, 1997_ **

** _FBI HQ_ **

“Sir? Agents Kinsley and Stonecypher are here for the seminar report,” Arlene’s voice sounded on his intercom.

He hadn’t yet got used to her treating him so politely at work, but they had both agreed it should be done that way.

“Thanks, Arlene,” Walter answered quickly. “Let them in.”

Soon, the pair was entering his space and sitting in front of him. Walter went through the report and wasn’t surprised to read about his _favorite_ pair.

“So, Agents Mulder and Scully didn’t make it to the seminar.”

“No, sir. They caught a case in Leon County and decided it was more important than _stacking chairs_,” Agent Kinsley said, surely mocking something Agent Mulder had commented on.

“To be fair, they saved a parent and a local officer. So maybe… they were right to stop by,” Agent Stonecypher added quickly.

“That’s okay, Agents, I’ll deal with them later.” Walter was slightly angry. He had put the four of them together in an ultimate attempt to get agent Mulder to the teamwork seminar. Somehow he understood that next time he would have to cuff him and drive Mulder himself if he was to make sure that he finally attended one of those.

“Walter?” Arlene’s worried voice suddenly sounded on the intercom.

“Anything wrong?” He found himself getting concerned. She never called him that at work.

“I think my water broke—”

She didn’t need to finish the sentence. A millisecond later, he was at the door, for a moment forgetting his coat on the rack. Lucky Mulder wouldn’t be getting his reprimand after all.

* * *

** _November 2, 1998_ **

** _FBI HQ_ **

“Ready to leave?” Arlene knocked on his door, handbag on her shoulder.

“Sure, just give me five minutes to organize this and we can be on our way,” Walter replied, fumbling with the folders piling on his desk

“Great. I’ll go get Johnny in the meantime.”

Walter relaxed a little. If she went to get the kid by herself, he got some extra ten minutes, while she talked to the nursery lady. His load of work had decreased exponentially since he didn’t need to take care of The X-Files reports and, especially, complaints. But he still had hundreds of agents who required his supervision. Those others were not so happy lately since he was more on their backs than usual. Walter looked at the three piles of folders. If he worked hard, maybe he could get his desk cleared before New Year’s Eve for the first year in a while.

“Walter?” Arlene was back sooner than expected, and looking completely startled. “J—Judy says y—you picked up Johnny an… hour ago?”

This couldn’t be happening. 

+++++++

Walter decided to send Arlene home with the promise that he would be back soon with their kid. Having her around, sobbing and worrying wasn’t helping. And he couldn’t take her where he was going. There was no need for her to see the troubles he’d go through, what he would do to get his little boy back.

The security camera clearly showed him picking up the baby from the nursery, so immediately he knew where to turn to. Third call to Mulder and he wasn’t answering the phone. Where the hell was he?

“Mulder?” Walter’s voice faltered on the answering machine. He was getting angrier by the minute. “They took the kid. Mulder, They took my child!”

The Smoking Man had sworn it hadn’t been their making. Of course, he wouldn’t believe him, the lying bastard. If he had his new address, he’d be beating the answer out of him already. “That’s what happens when you play with fire, Walter,” he chuckled before hanging up the phone.

Without a lead to follow, he’d started to drive around the city to try and clear his mind, thinking about which door to pound next. The phone started ringing.

“Mr. Skinner?” an unknown voice answered on the other side of the line. “It is my belief that you have lost something… someone?”

With a quick swerve of the wheel that produced a couple of honks, he parked on the sidewalk.

“Who are you and what do you want with my kid?!” Walter yelled at the phone, ignoring the passers-by yelling at him as he took off up the sidewalk.

“Relax, Mr. Skinner, the kid is alright. He’ll be returned with no harm if you do a little something for us.”

“I’m listening.”

“Gibson Praise in exchange for your son. It should be easy. Your agents seem to be guarding him. I’ll call back in a couple of hours.”

The call went dead and Walter revved up without looking back. Arizona. He had sent them there this morning. It had to be connected somehow. 

+++++++

On the five hour flight, he had a lot to think about. Mulder wouldn’t hand over Gibson. Walter knew he shouldn’t be asking either. _We don’t negotiate with terrorists_, he repeated himself. But it was Johnny he had to look after first.

Upon landing, he managed to talk to Agent Scully. She was taking the kid to a medical center, the poor boy was in great pain and badly hurt. But when he got there, Gibson was already gone.

“I just looked away for a second!” Agent Scully was infuriated. The doctors around her were trying to calm her down, but it was only incensing her more.

Walter breathed for a second. So, _They_ had gotten to the kid first. It would be alright, he was going to get Johnny back. His phone rang. They were going to tell him where to pick him up. Everything would be alright.

“So, Mr. Skinner, I take it that you have Gibson ready for us,” the voice asked.

“You got him already, now I want my son back,” he yelled at the phone, walking away from Agent Scully. If she knew what was going on, she’d be the first to smack him hard. “Tell your smoking-son-of-a-bitch boss that he’ll pay dearly for this,” he hissed, looking back at Scully.

“Oh, Mr. Skinner, you are so wrong. We still don’t have the kid, and the time is ticking. You better find him soon.”

The phone clicked again and he was left aghast. How many organizations there were after Gibson Praise?

Walking back to Scully, he overheard her talking on the phone. 

“—Mulder, wait, AD Skinner is here, maybe he can get in,” she jabbered before putting away the phone and turning to him. “Sir, Mulder has located Gibson at a nuclear plant, but they won’t let him in. Agent Fowley is denying him access. Maybe you could pull some strings—.”

“I’ve got it from here,” Walter answered, heading out. Scully started following him. “Maybe it would be best if you two stayed out of it,” he earnestly offered. 

“Yes, Sir. Thank you, Sir,” he heard at his back and the words hurt him, but he managed not to let it show. Walter had years of training for that. He hated lying to them, but Johnny came first.

+++++++

The outside of the power plant was in pandemonium. Mulder had already been sent away. He had probably listened to Scully’s good sense. Diana Fowley was running the show, it was not difficult to get inside.

“Gibson! Gibson!” he kept shouting along with the other dozen of agents. 

It took hours, everybody else had already given up, thinking the kid was most probably dead. But Skinner didn’t. He couldn’t fail Johnny.

The plant was now silent, only the sound of machinery breaking the tranquility. And that’s where the kid walked in front of him.

“You’ve been looking for me,” he said in his calm tone. “We gotta get your son before it’s too late.”

He was, what? Eight years old? The kid was so young, but he always acted like a grown man. Walter was so brokenhearted about the childhood Gibson had to endure. Special abilities that he hadn’t asked to, being kidnapped over and over again...

“Gibson, I don’t really wanna do this but—.”

“Save your excuses, Mr. Skinner. I know nobody cares about me anymore.” Gibson walked in front of him on their way out, clearly defeated by the situation.

+++++++

Soon enough they were at the meeting point. On a dark moonless night, he couldn’t clearly see the man on the other side of the bridge. In other circumstances he might have shot him, but not while he was holding his son. He was a clever guy.

“Don’t try anything weird, Mr. Skinner. Or both the kids die.”

Walter wasn’t at all surprised to see his own face on the man when he was closer. The stranger was holding his kid, asleep on his arms. At least the man had had the decency to keep a familiar face on so as not to disturb the child. He had to give him that.

Gibson was fidgeting by his side. Walter felt so guilty about giving him away, but he wanted his boy back. It didn’t feel honorable to sacrifice one child to save another. He thought about Mulder once again. _He would have found another way. It’s so dark, but maybe I can get a clear shot once…_

_“_The base of the neck,” Gibson responded to his inner thoughts. “Nowhere else will do.”

What was he talking about? Before Walter could ask him, Gibson started walking towards his double. As soon as the boy reached him, he saw his face change. It took him a moment to react. Mulder had written about that kind of thing several times on his reports, but Walter hadn’t believed a word of it. Alien Bounty Hunters, he had called them. Working for the alien race to erase any trace of their existence. They were real. Mulder was right. And he was letting a kid walk away with them. This was not right, he had to do something.

Walter was woken up from his reverie by a loud cry.

“Johnny!” he yelled and ran towards his son, who was lying in the middle of the road, alone and scared while the stranger and Gibson walked away. The stranger wouldn’t turn his back to him and was pointing a gun at Gibson’s temple. _The base of the neck_, Gibson’s words echoed in his mind. _I don’t need you to turn around to hit you, motherfucker._

Johnny was still crying at his feet, making him nervous. But Walter’s window of opportunity was closing rapidly. Unfastening his weapon, he aimed at the strangers Adam’s apple and shot without thinking twice. It would have to do.

The shot was deafening and Johnny stopped crying, only to resume a second later with even more strength. Walter grabbed his kid and hushed him as best he could while he ran towards Gibson, who had fallen to the ground dragged by the stranger. The image was so disturbing. The stranger’s face was dissolving rapidly into a puddle of radioactive green bubbles.

“Let’s get out of here,” Walter grabbed Gibson’s wrist and ran back to his car.

+++++++

He couldn’t get on a plane with the escaped kid, so starting his journey back through the desert seemed like the best idea. It gave him time to think. The aliens wanted Gibson, the Syndicate wanted him too. Surely, none of them had a nice plan in mind for him. The kid was on the most wanted list and Walter wouldn’t let him go to any of them.

“Thank you,” he uttered in the back seat.

“I thought you were sleeping, sorry.”

Walter tried to keep his thoughts to the minimum, the kid had told him how disturbed he was by the endless chatting.

“I was, but the sun woke me,” Gibson replied sitting up.

Walter could see him on the rearview mirror, looking at the sun showing up between the mountains with a languid smile.

“I haven’t seen the sun come out in ages,” the kid admitted and kept staring at the horizon.

“Do you want to stop for breakfast? I could use a little break,” Walter offered.

“Okay,” he answered, his eyes still focusing on the orange orb. 

Walter stopped at a simple gas station a couple of miles ahead and the three of them grabbed a bite. Gibson asked for a doughnut, Walter just had coffee. Johnny, still half-sleep on his father’s arms, munched on a piece of chocolate. They sat on the back of the station, relaxing a bit before they would continue their journey.

“What are you gonna do with me?” Gibson asked when they walked to the car, wiping some glaze on the corner of his mouth with the back of his hand.

“I still don’t know, Gibson,” Walter was surprised about the kid uttering that. He must know he’d been thinking about that for the past hours without reaching a clear conclusion. “We need to keep you safe, but I don’t know where you will be—.”

“I might have an idea,” the kid nodded to a sign on the road in the distance.

Walter squinted to read the words. School for the Deaf, Flemingtown, it said. It sounded like a great place. He’d be peaceful and out of reach. Yes, it could work.

**Author's Note:**

> Thanks for reading. Comments are always loved and appreciated :D


End file.
